*Protein ID (NP or XP #) or Wolbachia#: enter this info - Dr. B 090313
(use Summer13A Plate for Oligos instead of ordering new ones - Dr. B 090313))
091213 - also use the GDocs/Misc/Primers/DNAWorks_OutputSummer13 to get your correct DNA Works file for Tail Primer Design
*Organism (including strain):Trypanosoma cruzi Etiologic Risk Group (see link below):
*Background/Disease Information (sort of like the Intro to your Mini Research Write up): Chagas disease
Essentiality of this protein: Gene/Ortholog: Tb11.01.0450 (OG4_10262); Phenotype: significant loss of fitness in bloodstream forms (6 days); Source study: alsford
Complex of proteins?: No Druggable Target: Yes, Druggability index (range: 0 to 1): 0.6
*length of your protein in Amino Acids: 303 Amino Acids Molecular Weight: Predicted: 34417 Da Molar Extinction coefficient of your protein at 280 nm wavelength: TMpred graph Image (http://www.ch.embnet.org/software/TMPRED_form.html).
Do Not Need this info for Spring (but still copy these lines to your Target page for now) Primer design results for pNIC-Bsa4 cloning (list seqeunces of all of your ~40 nt long primers): (link to DNA Works output text file - that should be saved in your Google Docs folder after you did the primer design protocol)
-- Ask a mentor, Dr. B, or a fellow researcher -how to link a GDocs file if you are not sure how to.
Primer design results for 'tail' primers (this is just 2 sequences):
*NCBI Gene # or RefSeq#: EKF38512.1
http://www.ncbi.nlm.nih.gov/protein/EKF38512.1
*Protein ID (NP or XP #) or Wolbachia#: enter this info - Dr. B 090313
(use Summer13A Plate for Oligos instead of ordering new ones - Dr. B 090313))
091213 - also use the GDocs/Misc/Primers/DNAWorks_OutputSummer13 to get your correct DNA Works file for Tail Primer Design
*Organism (including strain): Trypanosoma cruzi
Etiologic Risk Group (see link below):
http://www.utexas.edu/research/rsc/ibc/agent_class.html#_Toc7238334
TDRTargets Link:
http://tdrtargets.org/targets/view?gene_id=44419
*Background/Disease Information (sort of like the Intro to your Mini Research Write up):
Chagas disease
Essentiality of this protein:
Gene/Ortholog: Tb11.01.0450 (OG4_10262); Phenotype: significant loss of fitness in bloodstream forms (6 days); Source study: alsford
Complex of proteins?: No
Druggable Target: Yes, Druggability index (range: 0 to 1): 0.6
*EC#: 3.1.3.16
Link to BRENDA EC# page: http://www.brenda-enzymes.org/php/result_flat.php4?ecno=3.1.3.16
Enzyme Assay information (spectrophotometric, coupled assay ?, reagents):
Spectrophotometric.
-- link to Sigma (or other company) page for assay or assay reagents (substrates)
-- link (or citation) to paper that contains assay information
-- List cost and quantity of substrate reagents and supplier
Structure Available (PDB or Homology model)
-- PDB # or closest PDB entry if using homology model: ??
-- For Homology Model option:
---- Query Coverage: 98%
---- Max % Identities: 76%
---- % Positives %
---- Chain used for homology:
Current Inhibitors:
Expression Information (has it been expressed in bacterial cells):
Purification Method:
Image of protein (PyMol with features delineated and shown separately):
*Amino Acid Sequence:
MSLDVDAIIDKLLGVRVSKPGKQVNLAENDVKNLALRSREILLAQPALLELEAPIKICGD
IHGQYYDLLRLFDNGGFPPSANYLFLGDYVDRGKQGLETICLVLAFKVKFPENFFLLRGN
HECASINRIYGFFDECKRRYNIRLWKAFTDTFNCLPVACIIDDKIFCCHGGLSPELQTMD
QIKRIARPCDVTDAGLICDLLWSDPEEGLSGWGENDRGVSYTFGQDIVEKFLRKHEFDLI
VRAHQVVEDGYQFFAKRQLITIFSAPNYCNEFDNSGAVMSVDADLLCSFQILKPSVKKPK
FYQ
*length of your protein in Amino Acids: 303 Amino Acids
Molecular Weight: Predicted: 34417 Da
Molar Extinction coefficient of your protein at 280 nm wavelength:
TMpred graph Image (http://www.ch.embnet.org/software/TMPRED_form.html).
*CDS Gene Sequence:
ATGTCCCTCGACGTTGACGCGATCATCGATAAACTGCTGGGTGTTCGTGTTTCTAAACCG
GGTAAACAAGTTAATCTGGCAGAAAATGACGTTAAAAACCTGGCGCTGCGTTCTCGTGAA
ATCCTCCTCGCGCAGCCAGCCCTGCTGGAACTGGAAGCGCCGATCAAGATCTGCGGTGAC
ATCCATGGTCAGTACTACGATCTCCTCCGCCTCTTCGACAACGGTGGTTTCCCGCCGTCT
GCGAATTACCTGTTCCTGGGTGACTACGTCGACCGCGGCAAGCAGGGTCTGGAGACCATC
TGCCTGGTTCTGGCGTTCAAAGTTAAATTCCCGGAAAACTTCTTCCTGCTGCGTGGCAAC
CATGAATGCGCGTCTATCAACCGTATCTATGGTTTCTTCGATGAATGTAAACGTCGCTAC
AACATCCGCCTGTGGAAAGCGTTCACCGACACGTTCAACTGCCTGCCTGTTGCCTGCATT
ATCGACGACAAAATCTTTTGCTGCCACGGCGGTCTGAGCCCGGAACTGCAGACTATGGAT
CAGATCAAACGTATCGCGCGTCCGTGCGATGTTACCGATGCGGGTCTGATCTGTGACCTG
CTGTGGTCTGACCCGGAGGAAGGTCTGTCTGGTTGGGGTGAAAACGACCGTGGCGTTTCT
TATACCTTCGGTCAGGACATCGTTGAAAAATTCCTGCGTAAGCACGAGTTCGACCTGATC
GTTCGTGCGCATCAGGTTGTTGAAGACGGTTACCAGTTCTTCGCAAAACGTCAGCTCATC
ACCATCTTCTCTGCGCCGAACTATTGCAACGAATTTGACAACTCTGGCGCGGTTATGTCT
GTCGACGCGGACCTCCTGTGCTCTTTTCAGATCCTGAAACCGAGCGTGAAAAAACCGAAA
TTCTATCAGTAA
*GC% Content for gene: %
Do Not Need this info for Spring (but still copy these lines to your Target page for now)
Primer design results for pNIC-Bsa4 cloning (list seqeunces of all of your ~40 nt long primers):
(link to DNA Works output text file - that should be saved in your Google Docs folder after you did the primer design protocol)
-- Ask a mentor, Dr. B, or a fellow researcher -how to link a GDocs file if you are not sure how to.
Primer design results for 'tail' primers (this is just 2 sequences):
References:
DVGGDIMNNDYIFLGDYVDRGYNSVETFEYLLLLKLLFPKNITLLRGNHESRQITTVYGF 127